A Three-Sample Test for Introgression.

abstract：:The genomes are folded in a complex three-dimensional (3D) structure. Some features of this organization are common for all eukaryotes, but little is known about its evolution. Here, we have studied the 3D organization and regulation of zebrafish globin gene domain and compared its organization and regulation with tho...

journal_title：Molecular biology and evolution

authors： Kovina AP,Petrova NV,Gushchanskaya ES,Dolgushin KV,Gerasimov ES,Galitsyna AA,Penin AA,Flyamer IM,Ioudinkova ES,Gavrilov AA,Vassetzky YS,Ulianov SV,Iarovaia OV,Razin SV

更新日期：2017-06-01 00:00:00

abstract：:The DnaK-DnaJ-GrpE (KJE) chaperone system functions at the fulcrum of protein homeostasis in bacteria. It interacts both with nascent polypeptides and with proteins that have become unfolded, either funneling its clients toward the native state or ushering misfolded proteins into degradation. In line with its key role...

journal_title：Molecular biology and evolution

authors： Warnecke T

更新日期：2012-11-01 00:00:00

abstract：:Despite the general assumption that site-specific mutation rates are independent of the local sequence context, a growing body of evidence suggests otherwise. To further examine context-dependent patterns of mutation, we amassed 5,645 spontaneous mutations in wild- type (WT) and mismatch-repair deficient (MMR(-)) muta...

journal_title：Molecular biology and evolution

authors： Sung W,Ackerman MS,Gout JF,Miller SF,Williams E,Foster PL,Lynch M

更新日期：2015-07-01 00:00:00

abstract：:In chickens, there is a single functional gene (VH1) coding for the heavy chain variable region of immunoglobulins, and immunoglobulin diversity is generated by gene conversion of the VH1 gene by many variable region pseudogenes (psi VH's) that exist on the 5' side of the VH1 gene. To understand the evolution of this ...

journal_title：Molecular biology and evolution

authors： Ota T,Nei M

更新日期：1995-01-01 00:00:00

abstract：:With growing amounts of genome data and constant improvement of models of molecular evolution, phylogenetic reconstruction became more reliable. However, our knowledge of the real process of molecular evolution is still limited. When enough large-sized data sets are analyzed, any subtle biases in statistical models ca...

journal_title：Molecular biology and evolution

authors： Kitazoe Y,Kishino H,Okabayashi T,Watabe T,Nakajima N,Okuhara Y,Kurihara Y

更新日期：2005-03-01 00:00:00

abstract：:Indirect tests have detected recombination in mitochondrial DNA (mtDNA) from many animal lineages, including mammals. However, it is possible that features of the molecular evolutionary process without recombination could be incorrectly inferred by indirect tests as being due to recombination. We have identified one s...

journal_title：Molecular biology and evolution

authors： Sun S,Evans BJ,Golding GB

更新日期：2011-09-01 00:00:00

abstract：:Cysteine-rich secretory proteins (CRISPs) are glycoproteins found exclusively in vertebrates and have broad diversified functions. They are hypothesized to play important roles in mammalian reproduction and in reptilian venom, where they disrupt homeostasis of the prey through several mechanisms, including among other...

journal_title：Molecular biology and evolution

authors： Sunagar K,Johnson WE,O'Brien SJ,Vasconcelos V,Antunes A

更新日期：2012-07-01 00:00:00

abstract：:The MIKC MADS-box gene family has been shaped by extensive gene duplications giving rise to subfamilies of genes with distinct functions and expression patterns. However, within these subfamilies the functional assignment is not that clear-cut, and considerable functional redundancy exists. One way to investigate the ...

journal_title：Molecular biology and evolution

authors： De Bodt S,Theissen G,Van de Peer Y

更新日期：2006-06-01 00:00:00

abstract：:Gene expression changes contribute to complex trait variations in both individuals and populations. However, the evolution of gene expression underlying complex traits over macroevolutionary timescales remains poorly understood. Snake venoms are proteinaceous cocktails where the expression of each toxin can be quantif...

journal_title：Molecular biology and evolution

authors： Barua A,Mikheyev AS

更新日期：2019-09-01 00:00:00

abstract：:Heterotypy is now recognized as a generative force in the formation of new proteins through modification of existing proteins. We report that heterotypy in the N-terminal region of the mature growth/differentiation factor 5 (GDF5) protein occurred during evolution of teleosts. N-terminal length variation of GDF5 was f...

journal_title：Molecular biology and evolution

authors： Fujimura K,Terai Y,Ishiguro N,Miya M,Nishida M,Okada N

更新日期：2008-05-01 00:00:00

abstract：:Recently, Lee et al. (Lee JH, Silhavy JL, Lee JE, et al. (30 co-authors). 2012. Evolutionarily assembled cis-regulatory module at a human ciliopathy locus. Science (335:966-969.) demonstrated that mutation in either of the transmembrane protein encoding genes, TMEM138 or TMEM216, causes phenotypically indistinguishabl...

journal_title：Molecular biology and evolution

authors： Venkatesh B,Ravi V,Lee AP,Warren WC,Brenner S

更新日期：2013-01-01 00:00:00

abstract：:In termites, as in many social insects, some individuals specialize in colony defense, developing diverse weaponry. As workers of the termite Neocapritermes taracua (Termitidae: Termitinae) age, their efficiency to perform general tasks decreases, while they accumulate defensive secretions and increase their readiness...

journal_title：Molecular biology and evolution

authors： Bourguignon T,Šobotník J,Brabcová J,Sillam-Dussès D,Buček A,Krasulová J,Vytisková B,Demianová Z,Mareš M,Roisin Y,Vogel H

更新日期：2016-03-01 00:00:00

abstract：:Proteins evolve not only through point mutations but also by insertion and deletion events, which affect the length of the protein. It is well known that such indel events most frequently occur in surface-exposed loops. However, detailed analysis of indel events in distantly related and fast-evolving proteins is hampe...

journal_title：Molecular biology and evolution

authors： Light S,Sagit R,Sachenkova O,Ekman D,Elofsson A

更新日期：2013-12-01 00:00:00

abstract：:Two longstanding issues on the molecular clock hypothesis are studied in this article. First, is there a global molecular clock in mammals? Although many authors have observed unequal rates of nucleotide substitution among mammalian lineages, some authors have proposed a global clock for all eutherians, i.e., a single...

journal_title：Molecular biology and evolution

authors： Yi S,Ellsworth DL,Li WH

更新日期：2002-12-01 00:00:00

abstract：:Purifying selection can substantially alter patterns of molecular evolution. Its main effect is to reduce overall levels of genetic variation, leading to a reduced effective population size. However, it also distorts genealogies relative to neutral expectations. A structured coalescent method has been used to describe...

journal_title：Molecular biology and evolution

authors： Nicolaisen LE,Desai MM

更新日期：2012-11-01 00:00:00

abstract：:The protein tyrosine phosphatase (PTP) family plays a central role in signal transduction pathways by controlling the phosphorylation state of serine, threonine, and tyrosine residues. PTPs can be divided into dual specificity phosphatases and the classical PTPs, which can comprise of one or two phosphatase domains. W...

journal_title：Molecular biology and evolution

authors： Pils B,Schultz J

更新日期：2004-04-01 00:00:00

abstract：:Coevolutionary conflict among imprinted genes that influence traits such as offspring growth may arise when maternal and paternal genomes have different evolutionary optima. This conflict is expected in outcrossing taxa with multiple paternity, but not self-fertilizing taxa. MEDEA (MEA) is an imprinted plant gene that...

journal_title：Molecular biology and evolution

authors： Miyake T,Takebayashi N,Wolf DE

更新日期：2009-04-01 00:00:00

abstract：:Marsupials exhibit great diversity in ecology and morphology. However, compared with their sister group, the placental mammals, our understanding of many aspects of marsupial evolution remains limited. We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of exta...

journal_title：Molecular biology and evolution

authors： Mitchell KJ,Pratt RC,Watson LN,Gibb GC,Llamas B,Kasper M,Edson J,Hopwood B,Male D,Armstrong KN,Meyer M,Hofreiter M,Austin J,Donnellan SC,Lee MS,Phillips MJ,Cooper A

更新日期：2014-09-01 00:00:00

abstract：:Most "tests of neutrality" assess whether particular data sets depart from the predictions of a standard neutral model with no recombination. For Drosophila, where nuclear polymorphism data routinely show evidence of genetic exchange, the assumption of no recombination is often unrealistic. In addition, while conserva...

journal_title：Molecular biology and evolution

authors： Przeworski M,Wall JD,Andolfatto P

更新日期：2001-03-01 00:00:00

abstract：:The occurrence of a fish-specific genome duplication (FSGD) in the lineage leading to teleost fishes is widely accepted, but the consequences of this event remain elusive. Teleosts, and the cichlid fishes from the species flocks in the East African Great Lakes in particular, evolved a unique complexity and diversity o...

journal_title：Molecular biology and evolution

authors： Braasch I,Salzburger W,Meyer A

更新日期：2006-06-01 00:00:00

abstract：:Various nucleotide substitution models have been developed to accommodate among lineage rate heterogeneity, thereby relaxing the assumptions of the strict molecular clock. Recently developed "uncorrelated relaxed clock" and "random local clock" (RLC) models allow decoupling of nucleotide substitution rates between des...

journal_title：Molecular biology and evolution

authors： Dornburg A,Brandley MC,McGowen MR,Near TJ

更新日期：2012-02-01 00:00:00

abstract：:Mitochondrial protein translation requires interactions between transfer RNAs encoded by the mitochondrial genome (mt-tRNAs) and mitochondrial aminoacyl tRNA synthetase proteins (mt-aaRS) encoded by the nuclear genome. It has been argued that animal mt-tRNAs have higher deleterious substitution rates relative to their...

journal_title：Molecular biology and evolution

authors： Adrion JR,White PS,Montooth KL

更新日期：2016-01-01 00:00:00

abstract：:A more than 10-fold difference in the specificity and catalytic efficiency for 1-naphthyl esters was measured between two allozymes of esterase-4 from Drosophila mojavensis. This difference is mainly caused by a difference in the affinity for the 1-naphthyl esters. The amino acid compositions of the allozymes are not ...

journal_title：Molecular biology and evolution

authors： Pen J,Schipper A,Rongen HA,Beintema JJ

更新日期：1986-07-01 00:00:00

abstract：:Because of the degeneracy of the genetic code, multiple codons are translated into the same amino acid. Despite being "synonymous," these codons are not equally used. Selective pressures are thought to drive the choice among synonymous codons within a genome, while GC content, which is typically attributed to mutation...

journal_title：Molecular biology and evolution

authors： Novoa EM,Jungreis I,Jaillon O,Kellis M

更新日期：2019-10-01 00:00:00

abstract：:We implement an isolation with migration model for three species, with migration occurring between two closely related species while an out-group species is used to provide further information concerning gene trees and model parameters. The model is implemented in the likelihood framework for analyzing multilocus geno...

journal_title：Molecular biology and evolution

authors： Zhu T,Yang Z

更新日期：2012-10-01 00:00:00

abstract：:Phenotypic convergence is an exciting outcome of adaptive evolution, occurring when different species find similar solutions to the same problem. Unraveling the molecular basis of convergence provides a way to link genotype to adaptive phenotypes, but can also shed light on the extent to which molecular evolution is r...

journal_title：Molecular biology and evolution

authors： Mendes FK,Hahn Y,Hahn MW

更新日期：2016-12-01 00:00:00

abstract：:Most mitochondrial proteins are synthesized in the cytosol of eukaryotic cells as precursor proteins carrying N-terminal extensions called transit peptides or presequences, which mediate their specific transport into mitochondria. However, plant cells possess a second potential target organelle for such transit peptid...

journal_title：Molecular biology and evolution

authors： Staiger C,Hinneburg A,Klösgen RB

更新日期：2009-08-01 00:00:00

abstract：:We measured nucleotide variability within and between the three semispecies of the Drosophila athabasca complex, at the period (per) gene by using a polymerase chain reaction-based four-cutter restriction-enzyme analysis. The levels of polymorphism varied considerably between the three semispecies. Our results for per...

journal_title：Molecular biology and evolution

authors： Ford MJ,Yoon CK,Aquadro CF

更新日期：1994-03-01 00:00:00

abstract：:Partial 18S rRNA sequence of the nemertine Cerebratulus lacteus was obtained and compared with those of coelomate metazoans and acoelomate platyhelminths to test whether nemertines share a most recent common ancestor with the platyhelminths, as traditionally has been implied, or whether nemertines lie within a protost...

journal_title：Molecular biology and evolution

authors： Turbeville JM,Field KG,Raff RA

更新日期：1992-03-01 00:00:00

abstract：:We report the complete sequence of a paralogous copy of elongation factor-1 alpha (EF-1 alpha) in the honeybee, Apis mellifera (Hymenoptera: Apidae). This copy differs from a previously described copy in the positions of five introns and in 25% of the nucleotide sites in the coding regions. The existence of two paralo...

journal_title：Molecular biology and evolution

authors： Danforth BN,Ji S

更新日期：1998-03-01 00:00:00